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Comparative genomics insight into phytopathogenic Xanthomonas arboricola pathovar corylina strains

Year 2021, Volume: 6 Issue: 1, 66 - 71, 31.03.2021
https://doi.org/10.35229/jaes.832315

Abstract

Xanthomonas arboricola pathovar corylina (Xac) causes a bacterial blight disease resulting in economic losses in young hazelnut trees worldwide. Although virulent Xac genomes were sequenced, there is no comparative genomics study on these genomes. In this study, all publicly available whole-genome sequences of Xac were compared by a comparative genomics approach. The results showed that Xac CFBP1159 and Xac CFBP2565 genomes are phylogenetically related to each other based on the orthology results. The genomic diversification of Xac strains was depended on mobile genetic elements. Interestingly, Xac NCCB100457 genome had additional motility genes than Xac CFBP1159 and Xac CFBP2565 genomes. All Xac genomes had shared virulence-related genes such as secretion systems and adherence factors. The comparative genomics approach of this study supports that Xac genomes have slight genetic variations, and the virulence-related proteins interacted with the host proteins. This comparative genomics approach will provide insights into the understanding of the Xac genomes.

References

  • Fischer-Le Saux, M., Bonneau, S., Essakhi, S., Manceau, C., Jacques, M.A.A. (2015). Aggressive emerging pathovars of Xanthomonas arboricola represent widespread epidemic clones distinct from poorly pathogenic strains, as revealed by multilocus sequence typing. Applied Environmental Microbiology 81, 4651–4668.
  • Barss, H.P. (1913). A new filbert disease in Oregon. Oregon Agricultural Experiment Station Biennial Crop Pest and Horticulture Report 14, 213–23.
  • EPPO, 2004. (2004). Diagnosis protocols for regulated pests Xanthomonas arboricola pv. corylina. EPPO Bulletin 34, 155–7.
  • Karahan, A., Altundağ, Ş., Duran, H., Kılınç, A.O. (2013). Karadeniz Bölgesinde Fındık Bakteriyel Yanıklığı [Xanthomonas arboricola pv. corylina (Miller et al.) Vauterin et al.] hastalığının yaygınlığı üzerine araştırmalar. Bitki Koruma Bülteni 2013, 53(3):159-174.
  • Lamichhane, J.R., Varvaro, L. (2014). Xanthomonas arboricola disease of hazelnut: current status and future perspectives for its management. Plant Pathology. 2014 Apr;63(2):243-254.
  • Timilsina, S., Potnis, N., Newberry, E.A., Liyanapathiranage, P., Iruegas-Bocardo, F., White, F.F., Goss, M.M., Jones, J.B. (2020). Xanthomonas diversity, virulence and plant–pathogen interactions. Nature Reviews Microbiology 18, 415–427 (2020).
  • Garita, C.J., Palacio-Bielsa, A., López, M.M., Cubero, J. (2017). Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors. Frontiers in Microbiology 8:573.
  • Alikhan, N.F., Petty, N.K., Ben Zakour, N.L., Beatson, S.A. (2011). Blast ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011;12:402.
  • Wang, Y., Coleman-Derr, D., Chen, G., Gu, Y.Q. (2015). OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research 2015;43:W78–W84.
  • Angiuoli, S.V., Gussman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D., Kyrpides, N., Madupu, R., Markowitz, V., Tatusova, T., Thomson, N., White, Owen. (2008). Toward an online repository of Standard Operating Procedures (SOPs) for (meta) genomic annotation. OMICS 12: 137-141.
  • Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., Edwards, R.A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A.R., Xia, F., Stevens, R. (2014). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research 42: 206-214.
  • Kumar, R., and Nanduri, B. (2010). HPIDB - a unified resource for host-pathogen interactions. BMC Bioinformatics 11 Suppl 6: S16.
  • Ammari, M.G., Gresham, C.R., McCarthy, F.M., and Nanduri, B. (2016). HPIDB 2.0: a curated database for host-pathogen interactions. Database (Oxford) 2016.
  • Lihong, C., Dandan, Z., Bo, L., Jian, Y., Qi, J. (2016). VFDB 2016: hierarchical and refined dataset for big data analysis–10 years on, Nucleic Acids Research. 44 (2016) D694–D697.
  • Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 41: 95-98.
  • Durmus, S., Cakir, T., Ozgur, A., and Guthke, R. (2015). A review on computational systems biology of pathogen-host interactions. Frontiers in Microbiology 6: 235.
  • Wu, H.J., Wang, A.H.J., Jennings, M.P. (2008). Discovery of virulence factors of pathogenic bacteria. Current Opinion in Chemical Biology, 12 (2008) 93–101. Hajri, A., Pothier, J.F., Saux, M.F.L. Bonneau, S., Poussier, S., Boureau, T., Duffy, B., Manceau, C. (2011). Type Three Effector Gene Distribution and Sequence Analysis Provide New Insights into the Pathogenicity of Plant-Pathogenic Xanthomonas arboricola. Applied and Environmental Microbiology Dec 2011, 78 (2) 371-384;
  • Jacques, M.A., Arlat, M., Boulanger, A., Boureau, T., Carrère, S., Cesbron, S., Chen, N.W., Cociancich, S., Darrasse, A., Denancé, N., Fischer-Le Saux, M., Gagnevin, L., Koebnik, R., Lauber, E., Noël, L.D., Pieretti, I., Portier, P., Pruvost, O., Rieux, A., Robène, I., Royer, M., Szurek, B., Verdier, V., Vernière, C. (2016). Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas. Annual Reviews Phytopathology 2016 Aug 4;54:163-87.
  • Szczesny, R., Jordan, M., Schramm, C., Schulz, S., Cogez, V., Bonas, U., Büttner, D. (2010). Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria. New Phytologist. 2010 Sep;187(4):983-1002.
  • Caballero, J.I., Zerillo, M.M., Snelling, J., Boucher, C., Tisserat, N. (2013). Genome Sequence of Xanthomonas arboricola pv. corylina, Isolated from Turkish Filbert in Colorado Genome Announcement. 2013 May 23; 1(3):e00246-13.

Fitopatojenik Xanthomonas arboricola pathovar corylina suşlarına karşılaştırmalı genomik bakış

Year 2021, Volume: 6 Issue: 1, 66 - 71, 31.03.2021
https://doi.org/10.35229/jaes.832315

Abstract

Xanthomonas arboricola pathovar corylina (Xac), Dünya çapında genç fındık ağaçlarında ekonomik kayıplarla sonuçlanan fındık bakteriyel yanıklığı hastalığına neden olmaktadır. Virülent Xac suşlarının tüm genomları dizilenmiş olmasına rağmen, bu genomlar üzerinde bir karşılaştırmalı genomik çalışma henüz yoktur. Bu çalışmada, Xac suşlarının halka açık tüm genom dizileri, karşılaştırmalı genomik yaklaşım kullanılarak karşılaştırılmıştır. Elde edilen sonuçlarda, Xac CFBP1159 ve Xac CFBP2565 genomlarının, ortoloji sonucuna göre filogenetik olarak birbirleriyle daha yakın ilişkili olduğu saptanmıştır. Xac suşlarının genomik çeşitliliğinin mobil genetik elementlerle ilişkişi olduğu anlaşılmıştır. İlginç bir şekilde, Xac NCCB100457 genomu, Xac CFBP1159 ve Xac CFBP2565 genomlarından daha fazla motilite genlerine sahiptir. Tüm Xac genomları, sekresyon sistemleri ve adhezyon faktörleri gibi virülans ile ilgili ortak genlere sahiptir. Bu çalışmanın karşılaştırmalı genomik yaklaşımı, Xac genomlarının bazı genetik varyasyonlara sahip olduğu ve virülans ile ilgili proteinlerin konakçı proteinlerle etkileşime girdiğini desteklemektedir. Bu çalışmanın karşılaştırmalı genomik yaklaşımı, Xac genomlarının anlaşılması için bir öngörü sağlamıştır.

References

  • Fischer-Le Saux, M., Bonneau, S., Essakhi, S., Manceau, C., Jacques, M.A.A. (2015). Aggressive emerging pathovars of Xanthomonas arboricola represent widespread epidemic clones distinct from poorly pathogenic strains, as revealed by multilocus sequence typing. Applied Environmental Microbiology 81, 4651–4668.
  • Barss, H.P. (1913). A new filbert disease in Oregon. Oregon Agricultural Experiment Station Biennial Crop Pest and Horticulture Report 14, 213–23.
  • EPPO, 2004. (2004). Diagnosis protocols for regulated pests Xanthomonas arboricola pv. corylina. EPPO Bulletin 34, 155–7.
  • Karahan, A., Altundağ, Ş., Duran, H., Kılınç, A.O. (2013). Karadeniz Bölgesinde Fındık Bakteriyel Yanıklığı [Xanthomonas arboricola pv. corylina (Miller et al.) Vauterin et al.] hastalığının yaygınlığı üzerine araştırmalar. Bitki Koruma Bülteni 2013, 53(3):159-174.
  • Lamichhane, J.R., Varvaro, L. (2014). Xanthomonas arboricola disease of hazelnut: current status and future perspectives for its management. Plant Pathology. 2014 Apr;63(2):243-254.
  • Timilsina, S., Potnis, N., Newberry, E.A., Liyanapathiranage, P., Iruegas-Bocardo, F., White, F.F., Goss, M.M., Jones, J.B. (2020). Xanthomonas diversity, virulence and plant–pathogen interactions. Nature Reviews Microbiology 18, 415–427 (2020).
  • Garita, C.J., Palacio-Bielsa, A., López, M.M., Cubero, J. (2017). Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors. Frontiers in Microbiology 8:573.
  • Alikhan, N.F., Petty, N.K., Ben Zakour, N.L., Beatson, S.A. (2011). Blast ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011;12:402.
  • Wang, Y., Coleman-Derr, D., Chen, G., Gu, Y.Q. (2015). OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research 2015;43:W78–W84.
  • Angiuoli, S.V., Gussman, A., Klimke, W., Cochrane, G., Field, D., Garrity, G., Kodira, C.D., Kyrpides, N., Madupu, R., Markowitz, V., Tatusova, T., Thomson, N., White, Owen. (2008). Toward an online repository of Standard Operating Procedures (SOPs) for (meta) genomic annotation. OMICS 12: 137-141.
  • Overbeek, R., Olson, R., Pusch, G.D., Olsen, G.J., Davis, J.J., Disz, T., Edwards, R.A., Gerdes, S., Parrello, B., Shukla, M., Vonstein, V., Wattam, A.R., Xia, F., Stevens, R. (2014). The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Research 42: 206-214.
  • Kumar, R., and Nanduri, B. (2010). HPIDB - a unified resource for host-pathogen interactions. BMC Bioinformatics 11 Suppl 6: S16.
  • Ammari, M.G., Gresham, C.R., McCarthy, F.M., and Nanduri, B. (2016). HPIDB 2.0: a curated database for host-pathogen interactions. Database (Oxford) 2016.
  • Lihong, C., Dandan, Z., Bo, L., Jian, Y., Qi, J. (2016). VFDB 2016: hierarchical and refined dataset for big data analysis–10 years on, Nucleic Acids Research. 44 (2016) D694–D697.
  • Hall, T. A. (1999). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series. 41: 95-98.
  • Durmus, S., Cakir, T., Ozgur, A., and Guthke, R. (2015). A review on computational systems biology of pathogen-host interactions. Frontiers in Microbiology 6: 235.
  • Wu, H.J., Wang, A.H.J., Jennings, M.P. (2008). Discovery of virulence factors of pathogenic bacteria. Current Opinion in Chemical Biology, 12 (2008) 93–101. Hajri, A., Pothier, J.F., Saux, M.F.L. Bonneau, S., Poussier, S., Boureau, T., Duffy, B., Manceau, C. (2011). Type Three Effector Gene Distribution and Sequence Analysis Provide New Insights into the Pathogenicity of Plant-Pathogenic Xanthomonas arboricola. Applied and Environmental Microbiology Dec 2011, 78 (2) 371-384;
  • Jacques, M.A., Arlat, M., Boulanger, A., Boureau, T., Carrère, S., Cesbron, S., Chen, N.W., Cociancich, S., Darrasse, A., Denancé, N., Fischer-Le Saux, M., Gagnevin, L., Koebnik, R., Lauber, E., Noël, L.D., Pieretti, I., Portier, P., Pruvost, O., Rieux, A., Robène, I., Royer, M., Szurek, B., Verdier, V., Vernière, C. (2016). Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas. Annual Reviews Phytopathology 2016 Aug 4;54:163-87.
  • Szczesny, R., Jordan, M., Schramm, C., Schulz, S., Cogez, V., Bonas, U., Büttner, D. (2010). Functional characterization of the Xcs and Xps type II secretion systems from the plant pathogenic bacterium Xanthomonas campestris pv vesicatoria. New Phytologist. 2010 Sep;187(4):983-1002.
  • Caballero, J.I., Zerillo, M.M., Snelling, J., Boucher, C., Tisserat, N. (2013). Genome Sequence of Xanthomonas arboricola pv. corylina, Isolated from Turkish Filbert in Colorado Genome Announcement. 2013 May 23; 1(3):e00246-13.
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Details

Primary Language English
Journal Section Articles
Authors

Şafak Kalındamar 0000-0003-2897-9911

Publication Date March 31, 2021
Submission Date November 27, 2020
Acceptance Date February 1, 2021
Published in Issue Year 2021 Volume: 6 Issue: 1

Cite

APA Kalındamar, Ş. (2021). Comparative genomics insight into phytopathogenic Xanthomonas arboricola pathovar corylina strains. Journal of Anatolian Environmental and Animal Sciences, 6(1), 66-71. https://doi.org/10.35229/jaes.832315


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